His sister Florence Augusta Merriam Bailey was a pioneering ornithologist who introduced popular field guides for bird identification. She married Vernon Bailey a field naturalist and long-time collecting partner of C. Hart Merriam's. His grandson Lee Merriam Talbot (born 1930) was a geographer and ecologist who was among the IUCN team which rediscovered the Persian Fallow Deer in 1957, and secretary general of the IUCN from 1980 to 1983.

Later in life, funded by the Harriman family, Merriam's focus shifted to studying and assisting the Native American tribes in the western United States. His contributions on the myths of central California and on ethnogeography were particularly noteworthy.